+Open data
-Basic information
Entry | Database: PDB / ID: 8wey | ||||||
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Title | PSI-LHCI of the red alga Cyanidium caldarium RK-1 (NIES-2137) | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / Photosystem I / ELECTRON TRANSPORT | ||||||
Function / homology | : / BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Unknown ligand Function and homology information | ||||||
Biological species | Cyanidium caldarium (eukaryote) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.92 Å | ||||||
Authors | Kato, K. / Hamaguchi, T. / Nakajima, Y. / Kawakami, K. / Yonekura, K. / Shen, J.R. / Nagao, R. | ||||||
Funding support | 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2024 Title: The structure of PSI-LHCI from provides evolutionary insights into conservation and diversity of red-lineage LHCs. Authors: Koji Kato / Tasuku Hamaguchi / Minoru Kumazawa / Yoshiki Nakajima / Kentaro Ifuku / Shunsuke Hirooka / Yuu Hirose / Shin-Ya Miyagishima / Takehiro Suzuki / Keisuke Kawakami / Naoshi Dohmae / ...Authors: Koji Kato / Tasuku Hamaguchi / Minoru Kumazawa / Yoshiki Nakajima / Kentaro Ifuku / Shunsuke Hirooka / Yuu Hirose / Shin-Ya Miyagishima / Takehiro Suzuki / Keisuke Kawakami / Naoshi Dohmae / Koji Yonekura / Jian-Ren Shen / Ryo Nagao / Abstract: Light-harvesting complexes (LHCs) are diversified among photosynthetic organisms, and the structure of the photosystem I-LHC (PSI-LHCI) supercomplex has been shown to be variable depending on the ...Light-harvesting complexes (LHCs) are diversified among photosynthetic organisms, and the structure of the photosystem I-LHC (PSI-LHCI) supercomplex has been shown to be variable depending on the species of organisms. However, the structural and evolutionary correlations of red-lineage LHCs are unknown. Here, we determined a 1.92-Å resolution cryoelectron microscopic structure of a PSI-LHCI supercomplex isolated from the red alga RK-1 (NIES-2137), which is an important taxon in the Cyanidiophyceae. We subsequently investigated the correlations of PSI-LHCIs from different organisms through structural comparisons and phylogenetic analysis. The PSI-LHCI structure obtained shows five LHCI subunits surrounding a PSI-monomer core. The five LHCIs are composed of two Lhcr1s, two Lhcr2s, and one Lhcr3. Phylogenetic analysis of LHCs bound to PSI in the red-lineage algae showed clear orthology of LHCs between and , whereas no orthologous relationships were found between Lhcr1-3 and LHCs in other red-lineage PSI-LHCI structures. These findings provide evolutionary insights into conservation and diversity of red-lineage LHCs associated with PSI. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wey.cif.gz | 907.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wey.ent.gz | 792.9 KB | Display | PDB format |
PDBx/mmJSON format | 8wey.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wey_validation.pdf.gz | 10.8 MB | Display | wwPDB validaton report |
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Full document | 8wey_full_validation.pdf.gz | 11.9 MB | Display | |
Data in XML | 8wey_validation.xml.gz | 236.1 KB | Display | |
Data in CIF | 8wey_validation.cif.gz | 289.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/we/8wey ftp://data.pdbj.org/pub/pdb/validation_reports/we/8wey | HTTPS FTP |
-Related structure data
Related structure data | 37480MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Photosystem I ... , 12 types, 12 molecules ABCDEFIJKLMO
#1: Protein | Mass: 82698.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) |
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#2: Protein | Mass: 82160.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) |
#3: Protein | Mass: 8822.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) |
#4: Protein | Mass: 15709.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) |
#5: Protein | Mass: 6974.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) |
#6: Protein | Mass: 20520.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) |
#7: Protein/peptide | Mass: 3408.183 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) |
#8: Protein/peptide | Mass: 4426.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) |
#9: Protein | Mass: 7105.433 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) |
#10: Protein | Mass: 15343.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) |
#11: Protein/peptide | Mass: 3010.698 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) |
#12: Protein | Mass: 16661.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) |
-Protein , 3 types, 5 molecules 14253
#13: Protein | Mass: 24117.104 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) #14: Protein | Mass: 24128.066 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) #15: Protein | | Mass: 23826.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) |
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-Sugars , 2 types, 8 molecules
#22: Sugar | ChemComp-LMT / #24: Sugar | ChemComp-DGD / | |
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-Non-polymers , 9 types, 790 molecules
#16: Chemical | ChemComp-CL0 / | ||||||||||||||
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#17: Chemical | ChemComp-CLA / #18: Chemical | #19: Chemical | #20: Chemical | ChemComp-BCR / #21: Chemical | #23: Chemical | ChemComp-UNL / Num. of mol.: 25 / Source method: obtained synthetically #25: Chemical | ChemComp-5X6 / ( Mass: 568.871 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C40H56O2 #26: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: PSI-LHCI / Type: COMPLEX / Entity ID: #1-#15 / Source: NATURAL | |||||||||||||||
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Molecular weight | Value: 0.55 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Cyanidium caldarium (eukaryote) | |||||||||||||||
Buffer solution | pH: 6.5 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 2.83 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R0.6/1 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 300 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 39.8 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 1.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 228449 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: RECIPROCAL | ||||||||||||||||||||||||||||||||||||
Atomic model building | Details: homology model / Source name: Other / Type: in silico model |